Puts Subdomain and Coefficients back into namespaces.

aurora-multiphysics · Jun 21, 2024 · a09e68b · a09e68b
1 parent db761cd
commit a09e68b
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Showing 74 changed files with 109 additions and 85 deletions.
diff --git a/include/auxkernels/MFEMAuxSolver.h b/include/auxkernels/MFEMAuxSolver.h
@@ -18,7 +18,7 @@ class MFEMAuxSolver : public GeneralUserObject
 
   inline virtual std::shared_ptr<platypus::AuxSolver> getAuxSolver() const { return _auxsolver; }
 
-  virtual void storeCoefficients(Coefficients & coefficients) {}
+  virtual void storeCoefficients(platypus::Coefficients & coefficients) {}
 
 protected:
   std::shared_ptr<platypus::AuxSolver> _auxsolver{nullptr};

diff --git a/include/auxkernels/MFEMJouleHeatingAux.h b/include/auxkernels/MFEMJouleHeatingAux.h
@@ -18,7 +18,7 @@ class JouleHeatingCoefficient : public platypus::CoupledCoefficient
   {
   }
 
-  void Init(const platypus::GridFunctions & variables, Coefficients & coefficients)
+  void Init(const platypus::GridFunctions & variables, platypus::Coefficients & coefficients)
   {
     // To ensure conductivity on subdomains is converted into global coefficient
     // Hephaestus update for coefficients initialisation could address this
@@ -71,7 +71,7 @@ class MFEMJouleHeatingAux : public MFEMAuxSolver
     return joule_heating_aux;
   }
 
-  virtual void storeCoefficients(Coefficients & coefficients) override;
+  virtual void storeCoefficients(platypus::Coefficients & coefficients) override;
 
 protected:
   platypus::InputParameters joule_heating_params;

diff --git a/include/auxsolvers/auxsolver_base.h b/include/auxsolvers/auxsolver_base.h
@@ -20,7 +20,8 @@ class AuxSolver
   // NB: require virtual destructor to avoid leaks.
   virtual ~AuxSolver() = default;
 
-  virtual void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) = 0;
+  virtual void Init(const platypus::GridFunctions & gridfunctions,
+                    platypus::Coefficients & coefficients) = 0;
 
   virtual void Solve(double t = 0.0) = 0;
 

diff --git a/include/auxsolvers/auxsolvers.h b/include/auxsolvers/auxsolvers.h
@@ -21,7 +21,7 @@ class AuxSolvers : public platypus::NamedFieldsMap<platypus::AuxSolver>
 private:
 public:
   std::vector<std::pair<std::shared_ptr<platypus::AuxSolver>, std::string>> _aux_queue;
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients);
+  void Init(const platypus::GridFunctions & gridfunctions, platypus::Coefficients & coefficients);
   void Solve(double t = 0.0);
 };
 

diff --git a/include/auxsolvers/coefficient_aux.h b/include/auxsolvers/coefficient_aux.h
@@ -15,7 +15,8 @@ class CoefficientAux : public AuxSolver
 
   ~CoefficientAux() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 
   virtual void BuildBilinearForm();
   virtual void BuildLinearForm();

diff --git a/include/auxsolvers/coupled_coefficient_aux.h b/include/auxsolvers/coupled_coefficient_aux.h
@@ -20,7 +20,8 @@ class CoupledCoefficient : public mfem::Coefficient, public AuxSolver
 
   ~CoupledCoefficient() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 
   double Eval(mfem::ElementTransformation & T, const mfem::IntegrationPoint & ip) override;
 

diff --git a/include/auxsolvers/curl_aux.h b/include/auxsolvers/curl_aux.h
@@ -12,7 +12,8 @@ class CurlAuxSolver : public AuxSolver
 
   ~CurlAuxSolver() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 
   void Solve(double t = 0.0) override;
 

diff --git a/include/auxsolvers/flux_monitor_aux.h b/include/auxsolvers/flux_monitor_aux.h
@@ -20,7 +20,8 @@ class FluxMonitorAux : public AuxSolver
 
   ~FluxMonitorAux() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 
   void Solve(double t = 0.0) override;
 

diff --git a/include/auxsolvers/l2_error_vector_aux.h b/include/auxsolvers/l2_error_vector_aux.h
@@ -16,7 +16,8 @@ class L2ErrorVectorPostprocessor : public AuxSolver
 
   ~L2ErrorVectorPostprocessor() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 
   void Solve(double t = 0.0) override;
 

diff --git a/include/auxsolvers/scaled_vector_gridfunction_aux.h b/include/auxsolvers/scaled_vector_gridfunction_aux.h
@@ -21,7 +21,8 @@ class ScaledVectorGridFunctionAux : public AuxSolver
 
   ~ScaledVectorGridFunctionAux() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
   virtual void BuildBilinearForm();
   virtual void BuildMixedBilinearForm();
   void Solve(double t = 0.0) override;

diff --git a/include/auxsolvers/vector_coefficient_aux.h b/include/auxsolvers/vector_coefficient_aux.h
@@ -14,7 +14,8 @@ class VectorCoefficientAux : public AuxSolver
 
   ~VectorCoefficientAux() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 
   virtual void BuildBilinearForm();
   virtual void BuildLinearForm();

diff --git a/include/auxsolvers/vector_gridfunction_cross_product_aux.h b/include/auxsolvers/vector_gridfunction_cross_product_aux.h
@@ -46,7 +46,8 @@ class VectorGridFunctionCrossProductAux : public VectorCoefficientAux
                                     std::string u_gf_name,
                                     std::string v_gf_name);
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 };
 
 } // namespace platypus
diff --git a/include/auxsolvers/vector_gridfunction_dot_product_aux.h b/include/auxsolvers/vector_gridfunction_dot_product_aux.h
@@ -61,7 +61,8 @@ class VectorGridFunctionDotProductAux : public CoefficientAux
 
   ~VectorGridFunctionDotProductAux() override = default;
 
-  void Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & gridfunctions,
+            platypus::Coefficients & coefficients) override;
 };
 
 } // namespace platypus
diff --git a/include/coefficients/MFEMParsedCoefficientHelper.h b/include/coefficients/MFEMParsedCoefficientHelper.h
@@ -52,7 +52,8 @@ class MFEMParsedCoefficientHelper : public MFEMCoefficient,
                      const std::vector<std::string> & constant_expressions,
                      const std::vector<std::string> & _mfem_coefficient_names,
                      const std::vector<std::string> & _mfem_gridfunction_names);
-  void Init(const platypus::GridFunctions & variables, Coefficients & coefficients) override;
+  void Init(const platypus::GridFunctions & variables,
+            platypus::Coefficients & coefficients) override;
 
   double Eval(mfem::ElementTransformation & trans, const mfem::IntegrationPoint & ip) override;
 

diff --git a/include/coefficients/coefficients.h b/include/coefficients/coefficients.h
@@ -6,6 +6,8 @@
 #include <memory>
 #include <unordered_set>
 
+namespace platypus
+{
 double prodFunc(double a, double b);
 double fracFunc(double a, double b);
 
@@ -20,7 +22,7 @@ class Subdomain
   platypus::NamedFieldsMap<mfem::VectorCoefficient> _vector_coefficients;
 };
 
-// Coefficients - stores all scalar and vector coefficients
+// platypus::Coefficients - stores all scalar and vector coefficients
 //--SetTime
 //--scalars
 //--vectors
@@ -43,3 +45,4 @@ class Coefficients
   platypus::NamedFieldsMap<mfem::VectorCoefficient> _vectors;
   std::vector<Subdomain> _subdomains;
 };
+} // namespace platypus
diff --git a/include/equation_systems/equation_system.h b/include/equation_systems/equation_system.h
@@ -67,7 +67,7 @@ class EquationSystem : public mfem::Operator
   virtual void Init(platypus::GridFunctions & gridfunctions,
                     const platypus::FESpaces & fespaces,
                     platypus::BCMap & bc_map,
-                    Coefficients & coefficients);
+                    platypus::Coefficients & coefficients);
   virtual void BuildLinearForms(platypus::BCMap & bc_map, platypus::Sources & sources);
   virtual void BuildBilinearForms();
   virtual void BuildMixedBilinearForms();

diff --git a/include/formulations/av_formulation.h b/include/formulations/av_formulation.h
@@ -42,7 +42,7 @@ class AVEquationSystem : public TimeDependentEquationSystem
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void AddKernels() override;
 
   std::string _a_name, _v_name, _coupled_variable_name, _alpha_coef_name, _beta_coef_name,

diff --git a/include/formulations/dual_formulation.h b/include/formulations/dual_formulation.h
@@ -42,7 +42,7 @@ class WeakCurlEquationSystem : public TimeDependentEquationSystem
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void AddKernels() override;
 
   std::string _h_curl_var_name, _h_div_var_name, _alpha_coef_name, _beta_coef_name,

diff --git a/include/formulations/hcurl_formulation.h b/include/formulations/hcurl_formulation.h
@@ -40,7 +40,7 @@ class CurlCurlEquationSystem : public TimeDependentEquationSystem
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void AddKernels() override;
 
   std::string _h_curl_var_name, _alpha_coef_name, _beta_coef_name, _dtalpha_coef_name;

diff --git a/include/kernels/curl_curl_kernel.h b/include/kernels/curl_curl_kernel.h
@@ -17,7 +17,7 @@ class CurlCurlKernel : public Kernel<mfem::ParBilinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParBilinearForm * blf) override;
   std::string _coef_name;
   mfem::Coefficient * _coef{nullptr};

diff --git a/include/kernels/diffusion_kernel.h b/include/kernels/diffusion_kernel.h
@@ -17,7 +17,7 @@ class DiffusionKernel : public Kernel<mfem::ParBilinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParBilinearForm * blf) override;
 
   std::string _coef_name;

diff --git a/include/kernels/kernel_base.h b/include/kernels/kernel_base.h
@@ -18,7 +18,7 @@ class Kernel
   virtual void Init(platypus::GridFunctions & gridfunctions,
                     const platypus::FESpaces & fespaces,
                     platypus::BCMap & bc_map,
-                    Coefficients & coefficients)
+                    platypus::Coefficients & coefficients)
   {
   }
 

diff --git a/include/kernels/mixed_vector_gradient_kernel.h b/include/kernels/mixed_vector_gradient_kernel.h
@@ -17,7 +17,7 @@ class MixedVectorGradientKernel : public Kernel<mfem::ParMixedBilinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParMixedBilinearForm * mblf) override;
   std::string _coef_name;
   mfem::Coefficient * _coef{nullptr};

diff --git a/include/kernels/vector_fe_mass_kernel.h b/include/kernels/vector_fe_mass_kernel.h
@@ -17,7 +17,7 @@ class VectorFEMassKernel : public Kernel<mfem::ParBilinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParBilinearForm * blf) override;
   std::string _coef_name;
   mfem::Coefficient * _coef{nullptr};

diff --git a/include/kernels/vector_fe_weak_divergence_kernel.h b/include/kernels/vector_fe_weak_divergence_kernel.h
@@ -17,7 +17,7 @@ class VectorFEWeakDivergenceKernel : public Kernel<mfem::ParMixedBilinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParMixedBilinearForm * mblf) override;
   std::string _coef_name;
   mfem::Coefficient * _coef{nullptr};

diff --git a/include/kernels/weak_curl_curl_kernel.h b/include/kernels/weak_curl_curl_kernel.h
@@ -17,7 +17,7 @@ class WeakCurlCurlKernel : public Kernel<mfem::ParLinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParLinearForm * lf) override;
 
   std::string _coupled_gf_name;

diff --git a/include/kernels/weak_curl_kernel.h b/include/kernels/weak_curl_kernel.h
@@ -17,7 +17,7 @@ class WeakCurlKernel : public Kernel<mfem::ParLinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParLinearForm * lf) override;
 
   std::string _hcurl_gf_name, _hdiv_gf_name;

diff --git a/include/materials/MFEMMaterial.h b/include/materials/MFEMMaterial.h
@@ -16,7 +16,7 @@ class MFEMMaterial : public GeneralUserObject
   virtual void initialize() override {}
   virtual void finalize() override {}
 
-  virtual void storeCoefficients(Subdomain & subdomain) {}
+  virtual void storeCoefficients(platypus::Subdomain & subdomain) {}
 
   std::vector<SubdomainName> blocks;
 };
diff --git a/include/problem/MFEMProblem.h b/include/problem/MFEMProblem.h
@@ -173,7 +173,7 @@ class MFEMProblem : public ExternalProblem
   std::string _formulation_name;
   int _order;
 
-  Coefficients _coefficients;
+  platypus::Coefficients _coefficients;
   platypus::InputParameters _solver_options;
   platypus::Outputs _outputs;
   platypus::InputParameters _exec_params;

diff --git a/include/problem_builders/problem_builder_base.h b/include/problem_builders/problem_builder_base.h
@@ -20,7 +20,7 @@ class Problem
 
   std::shared_ptr<mfem::ParMesh> _pmesh{nullptr};
   platypus::BCMap _bc_map;
-  Coefficients _coefficients;
+  platypus::Coefficients _coefficients;
   platypus::AuxSolvers _preprocessors;
   platypus::AuxSolvers _postprocessors;
   platypus::Sources _sources;
@@ -76,7 +76,7 @@ class ProblemBuilder
   void SetSolverOptions(platypus::InputParameters & solver_options);
   void SetJacobianPreconditioner(std::shared_ptr<mfem::Solver> preconditioner);
   void SetJacobianSolver(std::shared_ptr<mfem::Solver> solver);
-  void SetCoefficients(Coefficients & coefficients);
+  void SetCoefficients(platypus::Coefficients & coefficients);
 
   void AddFESpace(std::string fespace_name,
                   std::string fec_name,

diff --git a/include/sources/closed_coil.h b/include/sources/closed_coil.h
@@ -35,7 +35,7 @@ class ClosedCoilSolver : public platypus::Source
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParLinearForm * lf) override;
   void SubtractSource(mfem::ParGridFunction * gf) override;
 
@@ -85,7 +85,7 @@ class ClosedCoilSolver : public platypus::Source
   std::shared_ptr<mfem::Coefficient> _itotal{nullptr};
   std::vector<int> _old_dom_attrs;
   platypus::InputParameters _solver_options;
-  Coefficients _ccs_coefs;
+  platypus::Coefficients _ccs_coefs;
 
   // Here, we are solving for -(σ∇Va,∇ψ) = (σ∇Vt,∇ψ), where ∇Vt is grad_phi_t (within its relevant
   // mesh), ∇Va is grad_phi_aux, and their sum ∇Vt+∇Va is the full grad_phi, which is, up to an

diff --git a/include/sources/div_free_source.h b/include/sources/div_free_source.h
@@ -21,7 +21,7 @@ class DivFreeSource : public platypus::Source
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParLinearForm * lf) override;
   void SubtractSource(mfem::ParGridFunction * gf) override;
   void BuildHCurlMass();

diff --git a/include/sources/open_coil.h b/include/sources/open_coil.h
@@ -48,7 +48,7 @@ class OpenCoilSolver : public platypus::Source
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParLinearForm * lf) override;
   void SubtractSource(mfem::ParGridFunction * gf) override {};
 

diff --git a/include/sources/scalar_potential_source.h b/include/sources/scalar_potential_source.h
@@ -21,7 +21,7 @@ class ScalarPotentialSource : public platypus::Source
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override;
+            platypus::Coefficients & coefficients) override;
   void Apply(mfem::ParLinearForm * lf) override;
   void SubtractSource(mfem::ParGridFunction * gf) override;
   void BuildH1Diffusion(mfem::Coefficient * Sigma);

diff --git a/include/sources/source_base.h b/include/sources/source_base.h
@@ -20,7 +20,7 @@ class Source : public platypus::Kernel<mfem::ParLinearForm>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients) override
+            platypus::Coefficients & coefficients) override
   {
   }
 

diff --git a/include/sources/sources.h b/include/sources/sources.h
@@ -14,7 +14,7 @@ class Sources : public platypus::NamedFieldsMap<platypus::Source>
   void Init(platypus::GridFunctions & gridfunctions,
             const platypus::FESpaces & fespaces,
             platypus::BCMap & bc_map,
-            Coefficients & coefficients);
+            platypus::Coefficients & coefficients);
   void Apply(mfem::ParLinearForm * lf);
   void SubtractSources(mfem::ParGridFunction * gf);
 };

diff --git a/src/auxkernels/MFEMJouleHeatingAux.C b/src/auxkernels/MFEMJouleHeatingAux.C
@@ -20,7 +20,7 @@ MFEMJouleHeatingAux::MFEMJouleHeatingAux(const InputParameters & parameters)
 }
 
 void
-MFEMJouleHeatingAux::storeCoefficients(Coefficients & coefficients)
+MFEMJouleHeatingAux::storeCoefficients(platypus::Coefficients & coefficients)
 {
   coefficients._scalars.Register("JouleHeating", joule_heating_aux);
 }

diff --git a/src/auxsolvers/auxsolvers.C b/src/auxsolvers/auxsolvers.C
@@ -4,7 +4,8 @@ namespace platypus
 {
 
 void
-AuxSolvers::Init(const platypus::GridFunctions & gridfunctions, Coefficients & coefficients)
+AuxSolvers::Init(const platypus::GridFunctions & gridfunctions,
+                 platypus::Coefficients & coefficients)
 {
   for (const auto & [name, auxsolver] : *this)
   {
-Original file line number
+Diff line change
@@ Expand Up @@
     }
     void
-    MFEMJouleHeatingAux::storeCoefficients(Coefficients & coefficients)
+    MFEMJouleHeatingAux::storeCoefficients(platypus::Coefficients & coefficients)
     {
       coefficients._scalars.Register("JouleHeating", joule_heating_aux);
     }
@@ Expand Down @@